computeUnivariateTernaryMatrix: Compute the ternary matrix with digitized divergence coding

In divergence: Divergence: Functionality for assessing omics data by divergence with respect to a baseline

Description

Function for obtaining the ternary form for a matrix of data given a baseline range

Usage

computeUnivariateTernaryMatrix(seMat, Baseline)

Arguments

seMat	SummariziedExperiment with an assay in [0, 1], with each column corresponding to a sample and each row corresponding to a feature; usually in quantile form.
Baseline	A list with a data frame element "Ranges" containing the baseline range of each features; this corresponds to the output of findUnivariateGammaWithSupport() or computeUnivariateSupport()

Value

A matrix containing the ternary form data.

Examples

baseMat = breastTCGA_Mat[, breastTCGA_Group == "NORMAL"]
seMat.base = SummarizedExperiment(assays=list(data=baseMat))
assays(seMat.base)$quantile = computeQuantileMatrix(seMat.base)
baseline = computeUnivariateSupport(seMat=seMat.base)
dataMat = breastTCGA_Mat[, breastTCGA_Group != "NORMAL"]
seMat = SummarizedExperiment(assays=list(data=dataMat))
assays(seMat)$quantile = computeQuantileMatrix(seMat)
assays(seMat)$div = computeUnivariateTernaryMatrix(seMat=seMat, Baseline=baseline)

divergence documentation built on Nov. 8, 2020, 8:02 p.m.